Undergraduate Research Poster Day 2013

April 11, 2013

Six computer science undergraduates presented research projects April 11 during the third annual Computer Science Undergraduate Research Poster Day.

Selected to receive "Best Poster" recognition were:

  • Benjamin Berg for his project "Curve Simplification on the L2-Norm"
  • Derek Zhou for his project "The Effect of Chromatin Architecture on Gene Sequence Variation through Meiotic Recombination"

Receiving "Honorable Mention" were:

  • Yijia "Jimmy" Mu for his project "Electronic Conversion of Neuropsychological Tests for Minimal Hepatic Encephalopathy"
  • Afanasiy Yermakov for his project "Dynamic Hitting-Set and Set-Cover Algorithms"

Poster Day, held in the Levine Science Research Center's Hall of Science, recognizes the achievements of participants in the C-SURF program and other Graduation with Distinction candidates. Undergraduates are qualified to graduate with distinction if they have successfully completed a research independent study with faculty and an oral defense. In addition, Poster Day is intended to generate interest and enthusiasm for undergraduate research among faculty and students.

The students below described their work during the event as other students and faculty mingled through the Hall of Science viewing their posters and asking questions.


Benjamin Berg

Benjamin Berg worked with Professor Pankaj Agarwal to develop an algorithm to make efficient comparisons of large, inaccurate trajectory data sets possible by constructing small and accurate approximations of the underlying trajectories. His project built on previous research showing the type of approximation useful for comparing trajectories. Although that research described how to utilize such an approximation, it didn't show how to construct one efficiently. The changing accuracy of the data and trajectories with multiple directions called for constructing a continuous chain of lines to approximate a trajectory. Berg was able to construct a small set of candidate lines that might be used in an accurate approximation. Based on the determined set of candidate lines, an approximation that is close in error to the optimal approximation can be found. "This is a problem for which no result was previously known, so it provides a really good starting place," Berg said.

After graduation, Berg will work for a trading firm in Philadelphia, beginning in August.

View Benjamin Berg's poster


Chris Brown

Dwayne "Chris" Brown, working with Professor Susan Rodger, worked to integrate computer science into middle school mathematics using the 3D animated programming environment Alice. The goal is to expose more children to computer programming and computational skills in a format that is easy for teachers and administrators to use with existing curriculums.

For his project, Brown created free, downloadable Alice worlds with math games, such as "Basketball Math," which quizzes users' multiplication skills through a basketball game environment. He also created challenges in which students have to complete a world using math skills and programming. In the Distance Challenge, students must help the character Jimmy fulfill an adventure through various challenges, such as entering the correct formula for calculating the distance between two points. In addition, Brown helped map his worlds and other Alice worlds to Common Core standards for math in 5th-12th grades and the Computer Science Teachers Association's Level 2 standards for 6th-9th grades. He also helped create a free tutorial to assist teachers in building environments in Alice and helped provide Alice instruction to teachers and students through summer workshops for teachers in 2012 and an activity day for sixth-graders in March.

"There was a study done by the Computer Science Teachers Association that said that computer science education is at a crisis in the United States," Brown said. "Students are being exposed to more and more technology but not to how to make the technology."

Brown still is considering his post-graduation options, including software development and teaching. He has interviewed for a position to teach computer science to fifth- and sixth-graders at the University of Chicago's Chicago Laboratory Schools.

View Chris Brown's poster


Yijia Mu

Yijia "Jimmy" Mu worked with Computer Science Associate Chairman Richard Lucic to convert syndrome tests from paper to a tablet computer to test for hepatic encephalopathy. This form of liver failure - which results in confusion, an altered level of consciousness and coma - is not detected through basic psychiatric testing. Prior to his project, which was funded by Duke Clinical Research Institute, detection of hepatic encephalopathy occurred only through a series of cognitive tests used in paper form in Europe.

Mu used Xcode software development tools and an iOS framework to closely replicate the original six paper tests for use on an iPad. Benefits of the computerized form include automated timing and error detection, randomization of tests, and the ability to securely transfer and store data. Mu also added a survey at the end of the tests to check for any psychological conditions. Duke Clinical Research Institute is now testing his work, including assessing whether the tablet forms adhere to the statistical integrity of the original tests.

"We're trying to replicate the original tests as much as possible, but there are some design differences between our tests and their tests, so we're still in the process of clinical testing," Mu said.

Mu is interested in medicine but plans to work at Microsoft for a year before applying to medical schools.

View Yijia Mu's poster


Nikhil Saxena worked with Visiting Faculty Member Tabitha Peck to develop a virtual reality game in the Duke Immersive Virtual Environment (DiVE) to increase users' intuitive understanding of electromagnetics. "We believe that students have a better understanding of Newtonian mechanics than electromagnetics because they can easily visualize the forces in the world around them, such as gravity and friction," Saxena noted. He helped develop the game Field Goals, in C++ and OpenGL, to provide the same visualization capabilities in electromagnetic fields and forces as in Newtownian mechanics. Each level of Field Goals consists of a charged ball, a target, and various electric and magnetic fields. Users must launch the balls in such a way that they reach their targets despite the electromagnetic fields' effects.

The tool is currently being tested. Students participating in the research study complete a background survey to determine their prior experience with electromagnetics. They then play six levels of the game and take an exit survey to evaluate any change in their intuitive understanding of the field.

After graduation, Saxena will work as a back-end software engineer at the popular online review site Yelp.

View Nikhil Saxena's poster


Afanasiy Yermakov

Afanasiy Yermakov worked with Professor Pankaj Agarwal on dynamic algorithms for hitting-set and set-cover problems. "We want to efficiently maintain a small approximation," Yermakov noted in describing his work to allow for the fast handling of data modifications to such problems. In hitting-set problems, points are selected to hit all subsets of a set. Set-cover problems try to cover a set using the minimum number of subsets. For these problems in one dimension, instead of recomputing an optimal solution every time an insertion or deletion of data is made to the problem, Yermakov worked on algorithms that would guarantee a solution within some factor of the optimal at any point in time. Most of the time, updates would be handled locally and the solution would get a bit worse, but once the specified bound is reached a greedy algorithm would reconstruct the optimal solution. "It's a tradeoff," Yermakov said. "We can either have a very good solution that would take really long to compute, or we can have a slightly worse solution that we could do much, much faster."

Applications for the dynamic algorithm could include such hitting-set and set-cover problems as locating emergency facilities in a town, placing wireless routers in an airport or handling continuous query processing in a database.

After graduation, Yermakov will work in software engineering at Google in Mountain View, California.

View Afanasiy Yermakov's poster


Zhiyi "Jack" Zhang

Zhiyi "Jack" Zhang worked with Computer Science Lecturer Robert Duvall in investigating how to speed the process of grading computer science assignments at Duke and to offer more timely feedback to students. He noted many incoming students who are seeking degrees in other fields take computer science courses to gain marketable skills. With an influx of students and a curriculum that requires submission of assignments throughout the semester, feedback can be delayed. "Students submit assignments anticipating some kind of feedback that will help them with their next assignment, the midterm or just their general understanding of computer science," Zhang said.

To help ensure feedback remains relevant, he researched use of an automated system to generate feedback upon submittal of assignments and to help in grading. He found a variety of automated systems are available but many are input/output driven, making them incompatible with Duke's computer science curriculum. "Just looking at whether they've got a specific number of test cases correct doesn't mean they necessarily understand what they're doing," he said. Zhang created a basic framework for an automated system that examines input/output testing as well as looks for specific coding used to implement certain functions. He noted that even minor feedback is beneficial as students learn the mistakes they're making.

After graduation, Zhang will work in the software development track at Fidelity Investment in Morrisville, NC. He plans to apply to graduate schools in a year or two.

View Jack Zhang's poster


Derek Zhou

Derek Zhou worked with Professor Alexander Hartemink to determine how and why recombination of genetic material occurs at certain points in the DNA sequence. Genetic defects and the inheritance of diseases can be attributed to recombination - the process in which genetic material is broken and joined to other genetic material. "If we were able to discover the reason why recombination occurs at certain locations, we could really prevent certain genetically inherited diseases from occurring," Zhou said.

In his project, Zhou statistically analyzed hot and cold spots of DNA sequences - places with respectively higher and lower instances of recombination - and the alternating open reading frames and intergenic regions of those areas. What he found was almost no binding of transcription factors in cold spots but much higher levels of binding in hot spots, particularly in the open reading frames, or gene coding sequences. In addition, he found the transcription factors binding at higher levels in hot spots are coded for chromatin remodeling and loosening, essentially creating the same sense of openness found in intergenic regions. Drawing a biological conclusion, Zhou believes the openness - or creation of an unbound region of DNA - is necessary to allow a break in the double strand of DNA during meiosis, resulting in recombination.

"We want to say, 'Because this happens in the chromatin architecture, recombination happens,'" Zhou said, noting testing for causation of his findings still is needed. "If we're able to say that, then we could really begin to experimentally manipulate genetic sequences and see if we can eliminate or recreate recombination locations and then begin to affect genetically inherited diseases."

After graduation, Zhou will work as a trader for CitiGroup in New York.

View Derek Zhou's poster